NEWS

stressaddition 3.1.0 (2020-11-03)

Improved the documentation of the which argument in plot_survival() and plot_stress().
Changed the default value of the which argument in the plot functions. Now it contains the proper default curve names. If it is NA only the axes and labels will get drawn.

Added references to the journal article about the Multi-Tox model which was recently published.

Added missing return values in documentation to comply with CRAN repository policy.
Added a link to the paper in the description file.

Renamed all instances of "effect" to "survival".
Renamed all instances of "ec" to "lc".
Renamed predict_mixture(), which was a temporary development name, to multi_tox().
The argument proportion_ca in the mixture model multi_tox() was renamed and its value reversed. It is now called sa_contribution and specifies the proportion of stress addition in the calculation of toxicant stress. To convert your code from the old version use this equation: sa_contribution = 1 - proportion_ca.
Renamed stress_tox_sam to stress_tox_sa in the output of multi_tox().

Fixed a bug where plot_stress() with argument which = NULL would result in an error. Now it correctly draws the axes without data.
Fixed some errors in the documentation and improved the examples.

Exported function log10_ticks() for calculating tick mark labels and positions on a base 10 logarithmic axis.
Added example data set multiple_stress for use with multi_tox().
Various minor changes to prepare for CRAN submission.

The curves data frame in the output of ecxsys() now contains a column with the concentrations which are used for the plot functions in this package. This is useful for generating a nicer concentration axis.
Changes to ec():
- Renamed response_value to effect in the output list.
- response_level of 0 or 100 is now allowed. 0 returns the concentration 0 and 100 returns the concentration Inf. Previously this resulted in an error.
- It is now possible to set the reference to a custom value, for example 100.

Fixed unintended behaviour in plot_effect() and plot_stress() where supplying an empty vector caused the four standard curves to show. Now setting which to an empty vector or NULL shows just the axes. The default value is NA.
Renamed the mixture_effect column in the predict_mixture output data frame to effect.
Remove the restriction that the concentration vectors in predict_mixture() must be the same length. The longer length must be a multiple of the shorter length because the shorter vector gets recycled to the longer length.

Improved plot_effect() and plot_stress(). You can now control whether the observed values (the points) should be plotted using the which argument.
Renamed sys_tox_not_fitted and sys_tox_env_not_fitted to sys_tox_observed and sys_tox_env_observed in the output of ecxsys().

predict_mixture() now accepts multiple values for the concentration of the second toxicant. Both concentration vectors must be the same length.
predict_mixture() now returns a data frame with the concentrations and effects. Previously it was only a vector of effects.
predict_mixture() received a new argument "effect_max" which scales the returned effect values.
Renamed the arguments of predict_mixture() to use underscore letters a and b instad of 1 and 2. For example model_1 is now model_a.

ec() now raises an error if the curve does not cross the desired response level.
ecxsys() gained a new argument curves_concentration_max which allows setting the maximum concentration of the predicted curves.

Restore the default behaviour of plot_effect() to also show effect_tox and effect_tox_env.

The functions plot_effect() and plot_stress() gained a which argument that controls which curves are plotted. Consequently, the show_LL5_model argument of plot_effect() was removed.
Added arguments xlab and ylab to plot_stress.
Added argument main to both plot functions.
Changed some colors of the stress curves so they better match with the colors of related effect curves.
Added predict_mixture() for the prediction of the effects of mixtures of two toxicants.
Fixed documentation of ecxsys() and predict_ecxsys().

Changed the order of arguments in ecxsys().
Removed hormesis_index argument from ecxsys(). Use hormesis_concentration instead.
New function predict_ecxsys() replaces fn() from the ecxsys() output.
Renamed the arguments in ec().
Made ec() more flexible. It now also accepts a data.frame with a concentration column and a column of response values.
Added LL5 curves to the legend of plot_effect().
Replaced every occurrence of "simple" in variable names with "LL5".
Replaced every occurrence of "sys_stress" in variable names with "sys" because the extra "stress" was redundant.
Renamed plot_system_stress() to plot_stress() because it is planned to plot more stresses with this function in a future update.
Changed the order of the columns in the output of predict_ecxsys().
Improved the internal structure of the package.
Improved the tests.
Improved the documentation.